SNOMED

[Birger Haarbrandt]

Hi there,

I'm facing some trouble when trying to use stardog (2.2.1) with the OWL representation of SNOMED-CT (sct2_StatedRelationship_Snapshot_INT_20130731). I installed the trial version for developers on windows and ubuntu (both running on a quad core with 16GB RAM). Bulk-Load of SNOMED works fine (I'm also able to load the owl-file into Protege). On both systems it takes the query panel lots of time to show up. Sometimes it does not show up at all. It shows the same behaviour in recent versions of firefox, chrome and IE. The installation seems to be correct as a smaller ontology works smoothly and as expected.

When accessing via SNARL or CLI the database is responsive as long reasoning (EL, SL) is not involved. Using the mentioned reasoning types cause the following exception:

com.complexible.stardog.StardogException: GC overhead limit exceeded

at com.complexible.stardog.protocols.client.SPECClientUtil.toStardogException(SPECClientUtil.java:80)

at com.complexible.stardog.protocols.client.SPECClientUtil.toStardogException(SPECClientUtil.java:32)

at com.complexible.stardog.protocols.snarl.client.SNARLDriver.connect(SNARLDriver.java:142)

at com.complexible.stardog.api.DriverManager.getConnection(DriverManager.java:71)

at com.complexible.stardog.api.ConnectionConfiguration.connect(ConnectionConfiguration.java:137)

at Main.main(Main.java:46)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:601)

at com.intellij.rt.execution.application.AppMain.main(AppMain.java:120)

Caused by: com.complexible.common.protocols.client.ClientException: GC overhead limit exceeded

at com.complexible.common.protocols.client.rpc.DefaultRPCClient.get(DefaultRPCClient.java:344)

at com.complexible.common.protocols.client.rpc.DefaultRPCClient.execute(DefaultRPCClient.java:321)

at com.complexible.stardog.protocols.snarl.client.SNARLClientImpl.connect(SNARLClientImpl.java:130)

at com.complexible.stardog.protocols.snarl.client.SNARLClientImpl.connect(SNARLClientImpl.java:78)

at com.complexible.stardog.protocols.snarl.client.SNARLDriver.connect(SNARLDriver.java:126)

... 8 more

Caused by: java.lang.Exception: GC overhead limit exceeded

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

at java.lang.reflect.Constructor.newInstance(Constructor.java:525)

at com.complexible.barc.DefaultThrowableCodec.decode(DefaultThrowableCodec.java:89)

at com.complexible.barc.BigPacketCodec.toException(BigPacketCodec.java:393)

at com.complexible.barc.BigPacketCodec.decode(BigPacketCodec.java:360)

at com.complexible.barc.BigPacketDecoder.channelRead(BigPacketDecoder.java:75)

at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:332)

at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:318)

at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103)

at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:332)

at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:318)

at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:163)

at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:332)

at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:318)

at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:787)

at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:125)

at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:507)

at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:464)

at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:378)

at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:350)

at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)

at java.lang.Thread.run(Thread.java:722)

Afterwards, all databases seem to be deleted...

Please let me know if you need further information to get an idea what is going on.

Thank you,

Birger 

[Conrad Leonard]

The Java GC error suggests out of memory (and SNOMED is big). Have you increased the memory available using STARDOG_JAVA_ARGS Xmx settings?

[Birger Haarbrandt]

I increased from 6 to -Xmx10G. Now the reasoner does not cause the GC to throw this exception but I was not able to finish the reasoning within 10 hours...even though it might take a while, I guess that it takes a little too long. 

[Mike Grove]

On Fri, Oct 17, 2014 at 11:53 AM, Birger Haarbrandt <haarb...@googlemail.com> wrote:

I increased from 6 to -Xmx10G. Now the reasoner does not cause the GC to throw this exception but I was not able to finish the reasoning within 10 hours...even though it might take a while, I guess that it takes a little too long. 

What query are you attempting to run?

Cheers,

Mike

 

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[Birger Haarbrandt]

Hi Mike,

it's just a simple test query:

select ?s { ?s ?p ?o } LIMIT 10

To clarify, The query isn't reached by the program as it gets stuck beforehand. The connection looks like this:

Connection aConn = ConnectionConfiguration

                    .to("myDB")

                    .server("snarl://127.0.0.1:5820")

                    .credentials("admin", "admin")

                    .reasoning(ReasoningType.EL)

                    .connect()

                    .as(ReasoningConnection.class);
aConn.begin();

regards,

Birger

[Mike Grove]

This seems like the same problem Conrad is having with his ontology where it's taking longer than desired to classify the ontology.  We'll working on improving classification speed in an upcoming version of Stardog.

Cheers,

Mike

[geiste...@googlemail.com]

Hi Michael,

I'm testing the new version of Stardog. Obviously this issue has not been addressed in this released. Can you confirm that?

Cheers,

Birger 

[Mike Grove]

On Tue, Dec 2, 2014 at 8:44 AM, <geiste...@googlemail.com> wrote:

Hi Michael,

I'm testing the new version of Stardog. Obviously this issue has not been addressed in this released. Can you confirm that?

Correct.  SNOMED last I checked is about half a million classes, classification can be difficult.  We'll work on improving classification times for ontologies of this size at some point.

Cheers,

Mike

[Birger Haarbrandt]

Hi there,

sorry to bother you, have the performance issues of pellet been addressed in Stardog 3.0? 

Cheers,

Birger 

[Kendall Clark]

Probably the easiest way to figure this out is to download Stardog and run some queries and data through it.

Cheers,

Kendall

[haarbrandt]

Hi Kendall,

I thought that you might have an overview what has been fixed in the new release. Now I have the feeling that the problem causing the reasoner to fail on SNOMED is still unknown to you. Nevertheless, I will give it another shot. Thanks!

Best,

Birger

Am 25.03.2015 14:29 schrieb "Kendall Clark" <ken...@complexible.com>:
>
> Probably the easiest way to figure this out is to download Stardog and run some queries and data through it.
>
> Cheers,
> Kendall
>

> To unsubscribe from this group and stop receiving emails from it, send an email to stardog+u...@clarkparsia.com.

[Kendall Clark]

http://docs.stardog.com/RELEASE_NOTES.txt is complete.

I will say there can be a huge difference between was is known to *me* and what is known to everyone else who works on Stardog. In fact, that tends to be the ordinary state of affairs. :>

Cheers,

Kendall